Contacts of the helix formed by residues 298 - 307 (chain F) in PDB entry 7KHE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 298 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296F LYS* 3.0 18.6 - - + +
297F MET* 1.3 84.3 - - + +
299F LYS* 1.3 60.9 + - - +
300F LYS* 3.3 6.0 + - + +
301F ASN* 3.6 21.4 + - + +
302F PHE* 2.9 24.3 + - - +
326F TRP* 3.4 32.3 - - + +
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Residues in contact with LYS 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F MET* 5.8 3.8 - - + -
292F VAL* 3.4 51.9 + - + +
293F GLU* 4.6 8.6 + - - -
296F LYS 5.8 0.4 - - - -
297F MET 3.5 8.1 + - - -
298F PRO* 1.3 70.5 - - - +
300F LYS* 1.3 73.2 + - + +
302F PHE* 3.2 12.7 - - + +
303F ILE* 2.9 34.0 + - + +
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Residues in contact with LYS 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F PRO* 3.3 3.5 - - + -
299F LYS* 1.3 86.4 - - + +
301F ASN* 1.3 70.0 + - - +
303F ILE* 3.3 8.2 + - + +
304F THR* 3.0 25.6 + - - +
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Residues in contact with ASN 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F MET* 5.9 4.3 - - + -
298F PRO* 3.6 28.2 + - + +
300F LYS* 1.3 77.0 - - - +
302F PHE* 1.3 67.2 + - - +
304F THR* 3.3 12.7 - - + +
305F LEU* 2.9 35.8 + - + +
322F MET* 6.3 5.2 - - + -
326F TRP* 5.4 7.8 - - + -
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Residues in contact with PHE 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F GLU* 5.6 0.7 - - - -
288F MET* 3.1 55.6 - - + -
291F CYS* 5.4 1.3 - - + -
292F VAL* 3.9 12.1 - - + -
297F MET* 3.7 29.2 - - - +
298F PRO 2.9 17.2 + - - +
299F LYS* 3.2 24.2 - - + +
301F ASN* 1.3 74.5 - - - +
303F ILE* 1.3 80.0 + - + +
306F PHE* 2.9 63.8 + + + +
307F THR* 3.7 1.9 + - - -
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Residues in contact with ILE 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F LYS* 2.9 25.9 + - + +
300F LYS* 3.3 9.8 + - + +
302F PHE* 1.3 86.0 - - + +
304F THR* 1.3 68.1 + - - +
307F THR* 2.6 40.6 + - + +
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Residues in contact with THR 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F LYS 3.0 19.1 + - - +
301F ASN* 3.3 19.3 - - + +
303F ILE* 1.3 80.8 - - - +
305F LEU* 1.3 70.9 + - + +
307F THR* 3.6 11.6 - - - +
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Residues in contact with LEU 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F MET* 5.3 6.1 - - + -
301F ASN* 2.9 24.2 + - + +
304F THR* 1.3 79.0 - - + +
306F PHE* 1.3 64.5 + - - +
307F THR 3.5 4.3 + - - +
309F ASN* 3.8 8.8 + - - -
314F THR* 4.4 10.3 - - + +
315F TRP* 3.6 33.5 - - + +
318F ALA* 3.7 34.1 - - + -
319F ALA* 4.1 7.0 - - + +
322F MET* 4.1 15.9 - - + -
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Residues in contact with PHE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F GLU* 4.2 20.0 - - + -
287F ILE* 4.2 23.6 - - + -
288F MET* 4.6 3.8 - - + -
291F CYS* 6.3 1.3 - - - -
297F MET* 5.6 4.5 - - + +
301F ASN 3.9 0.2 + - - -
302F PHE* 2.9 62.0 + + + +
305F LEU* 1.3 76.7 - - - +
307F THR* 1.3 67.2 + - - +
309F ASN* 4.0 3.8 + - - +
310F GLU* 3.4 40.5 + - + +
315F TRP* 3.4 59.7 - + + -
341F LEU* 5.8 0.2 - - + -
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Residues in contact with THR 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F PHE* 4.0 1.9 + - - -
303F ILE* 2.6 43.5 + - + +
304F THR 3.6 11.4 - - - +
305F LEU 3.7 4.3 - - - +
306F PHE* 1.3 85.8 - - - +
308F GLY* 1.3 63.2 + - - +
309F ASN* 3.6 3.0 + - - -
310F GLU* 3.4 7.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il